Besides the upcoming Neverwinter Nights 2 and the already released Star Wars: KOTOR - Revenge of the Sith, Obsidian's John Morgan states on the Obsidian Forum that they are currently in pre-production of their third game. Most interesting is his comment about it not being a Bioware hand-me-down.

Obsidian Entertainment is indeed working on a third project. All I can really say is that it's in a state of pre-production at the moment and it is not a Bioware license.